[English] 日本語
Yorodumi
- PDB-1yfo: RECEPTOR PROTEIN TYROSINE PHOSPHATASE ALPHA, DOMAIN 1 FROM MOUSE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1yfo
TitleRECEPTOR PROTEIN TYROSINE PHOSPHATASE ALPHA, DOMAIN 1 FROM MOUSE
ComponentsRECEPTOR PROTEIN TYROSINE PHOSPHATASE ALPHA
KeywordsHYDROLASE / SIGNAL TRANSDUCTION / RECEPTOR / GLYCOPROTEIN / PHOSPHORYLATION
Function / homology
Function and homology information


NCAM signaling for neurite out-growth / RAF/MAP kinase cascade / regulation of focal adhesion assembly / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / synaptic membrane / integrin-mediated signaling pathway / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / insulin receptor signaling pathway ...NCAM signaling for neurite out-growth / RAF/MAP kinase cascade / regulation of focal adhesion assembly / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / synaptic membrane / integrin-mediated signaling pathway / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / insulin receptor signaling pathway / receptor complex / focal adhesion / membrane
Similarity search - Function
Receptor tyrosine-protein phosphatase alpha / Receptor tyrosine-protein phosphatase, alpha/epsilon-type / : / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic ...Receptor tyrosine-protein phosphatase alpha / Receptor tyrosine-protein phosphatase, alpha/epsilon-type / : / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Receptor-type tyrosine-protein phosphatase alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsBilwes, A.M. / Noel, J.P.
CitationJournal: Nature / Year: 1996
Title: Structural basis for inhibition of receptor protein-tyrosine phosphatase-alpha by dimerization.
Authors: Bilwes, A.M. / den Hertog, J. / Hunter, T. / Noel, J.P.
History
DepositionDec 11, 1996Processing site: BNL
Revision 1.0Apr 1, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RECEPTOR PROTEIN TYROSINE PHOSPHATASE ALPHA
B: RECEPTOR PROTEIN TYROSINE PHOSPHATASE ALPHA


Theoretical massNumber of molelcules
Total (without water)69,7902
Polymers69,7902
Non-polymers00
Water5,170287
1
A: RECEPTOR PROTEIN TYROSINE PHOSPHATASE ALPHA


Theoretical massNumber of molelcules
Total (without water)34,8951
Polymers34,8951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RECEPTOR PROTEIN TYROSINE PHOSPHATASE ALPHA


Theoretical massNumber of molelcules
Total (without water)34,8951
Polymers34,8951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.190, 119.840, 61.180
Angle α, β, γ (deg.)90.00, 110.08, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.999983, 0.001238, -0.005715), (0.001228, -0.999998, -0.001822), (-0.005717, 0.001814, -0.999982)
Vector: 0.134, -31.4184, 58.1333)

-
Components

#1: Protein RECEPTOR PROTEIN TYROSINE PHOSPHATASE ALPHA / D1


Mass: 34894.770 Da / Num. of mol.: 2 / Fragment: MEMBRANE PROXIMAL CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: TYPE I MEMBRANE PROTEIN / Cell line: BL21 / Cell line (production host): BL21 / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): 293 / References: UniProt: P18052, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRESIDUES 379 - 386 WERE NOT MODELLED FOR EACH MONOMER TRYPSIN CUT AT 385 OR 386.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 44 %
Crystal growpH: 5
Details: PROTEIN WAS CRYSTALLIZED FROM 12% PEG 8000 0.3 M AMMONIUM ACETATE, 50 MM SODIUM ACETATE PH 5, 2 MM DTT. ETHYLENE GLYCOL 20% WAS USED AS A CRYOPROTECTANT., pH 5.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115-20 mg/mlprotein1drop
250 mMsodium acetate1reservoir
30.3 Mammonium acetate1reservoir
412 %(w/v)PEG80001reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Jul 14, 1995 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→23 Å / Num. obs: 22317 / % possible obs: 82.4 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 27 Å2 / Rsym value: 0.046 / Net I/σ(I): 22
Reflection shellResolution: 2.25→2.35 Å / Redundancy: 1 % / Mean I/σ(I) obs: 7 / Rsym value: 0.104 / % possible all: 17.4
Reflection
*PLUS
Rmerge(I) obs: 0.046
Reflection shell
*PLUS
% possible obs: 17.4 % / Rmerge(I) obs: 0.104

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HNP

2hnp


Resolution: 2.25→20 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.251 -8.1 %RANDOM
Rwork0.184 ---
obs0.184 22277 82.4 %-
Refinement stepCycle: LAST / Resolution: 2.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4562 0 0 287 4849
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.16
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.19
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.25→2.35 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.324 -1.8 %
Rwork0.281 533 -
obs--17.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.16
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.19
LS refinement shell
*PLUS
Rfactor obs: 0.281

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more